BARABOO, Wis.(CHANNEL 3000) - St. John's Lutheran School in Baraboo is under federal investigation following a complaint over its policy toward LGBT students, officials confirmed Thursday.

At issue is the fact that St. John's receives federal dollars. The school gets funding for programs for school lunches, busing and through the No Child Left Behind Program.

The Madison-based Freedom From Religion Foundation, an organization that advocates for atheists and the separation of church and state, filed a complaint with the Wisconsin Department of Public Instruction May 10 after it received a letter school principal Craig Breitkreutz sent to parents in February, making them aware of changes for the upcoming school year. The DPI forwarded the complaint to the U.S. Department of Agriculture, which administers the school lunch program.

In the letter, Breitkreutz asked parents to sign an agreement that they and their child will support and obey the school's policy and that any violation could result in removal from the school. Breitkreuz said this protects the school's religious beliefs as well as its "ability to dismiss children that are not following (its) Christian faith."

In the letter, Breitkreutz said the school's federal funding complicates matters, as the acceptance of federal funds makes St. John's a Title IX school. He said the Office of Civil Rights, which protects the admittance of students at Title IX schools, looks for any cases of discrimination.

"The Office of Civil Rights now also protects discrimination against sexual preference and gender identification," the letter states. "If we cannot legally refuse students who are struggling with homosexuality or gender identification, we must maintain our right to hold to the truths of God's Word."

According to the letter, the school maintains the right to "discipline and dismiss" students who "(choose) an outwardly sinful lifestyle."

The letter also states: "(U)nfortunately, we must know the gender of your child. Although this last item should never be an issue, we must be aware to protect our religious freedom."